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https://github.com/chrovis/varity
Variant translation library for Clojure
https://github.com/chrovis/varity
bioinformatics clojure hgvs liftover vcf
Last synced: 3 days ago
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Variant translation library for Clojure
- Host: GitHub
- URL: https://github.com/chrovis/varity
- Owner: chrovis
- License: apache-2.0
- Created: 2017-04-18T09:17:40.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2024-10-17T23:10:22.000Z (28 days ago)
- Last Synced: 2024-10-19T14:08:59.123Z (27 days ago)
- Topics: bioinformatics, clojure, hgvs, liftover, vcf
- Language: Clojure
- Size: 825 KB
- Stars: 8
- Watchers: 13
- Forks: 2
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
Awesome Lists containing this project
README
# varity
[](https://clojars.org/varity)
[](https://github.com/chrovis/varity/actions/workflows/build.yml)
[](https://codecov.io/gh/chrovis/varity)
Variant translation library for Clojure.
## Features
* VCF variant ⇄ HGVS
* Finding HGVS aliases
* Conversion of a genomic coordinates between assemblies
## Installation
Clojure CLI/deps.edn:
```clojure
varity/varity {:mvn/version "0.11.0"}
```
Leiningen/Boot:
```clojure
[varity "0.11.0"]
```
To use varity with Clojure 1.8, you must include a dependency on
[clojure-future-spec](https://github.com/tonsky/clojure-future-spec).
## Breaking changes in 0.11.0
We fixed the `varity.vcf-to-hgvs` implementation.
It is confusing to throw the exception in `vcf-variant->protein-hgvs` when a variant overlaps the exon-intron boundaries, even if coding DNA HGVS is available. So we changed the behavior to return protein HGVS as `nil`.
## Usage
### Documentation
[API Reference](https://chrovis.github.io/varity/)
### Notice
All positions are represented as one-based number, and all ranges are
represented as one-based closed intervals. For example,
```clojure
{:pos 3}
```
represents the third position from the start, and
```clojure
{:chr "chr1", :start 1, :end 3}
```
represents the first three bases of chromosome 1.
### VCF variant to HGVS
`varity.vcf-to-hgvs` provides functions to convert a VCF-style variant into HGVS.
The returned HGVS is data structure of [clj-hgvs](https://github.com/chrovis/clj-hgvs).
```clojure
(require '[varity.vcf-to-hgvs :as v2h])
(v2h/vcf-variant->hgvs {:chr "chr7", :pos 55191822, :ref "T", :alt "G"}
"path/to/hg38.fa" "path/to/refGene.txt.gz")
;;=> ({:coding-dna #clj-hgvs/hgvs "NM_005228:c.2573T>G",
;; :protein #clj-hgvs/hgvs "p.L858R"})
```
Use `clj-hgvs.core/format` to obtain HGVS text.
```clojure
(require '[clj-hgvs.core :as hgvs])
(def l858r (-> (v2h/vcf-variant->protein-hgvs {:chr "chr7", :pos 55191822, :ref "T", :alt "G"}
"path/to/hg38.fa" "path/to/refGene.txt.gz")
first))
(hgvs/format l858r {:amino-acid-format :long})
;;=> "p.Leu858Arg"
```
### HGVS to VCF variants
`varity.hgvs-to-vcf` provides functions to convert HGVS into VCF-style variants.
```clojure
(require '[varity.hgvs-to-vcf :as h2v]
'[clj-hgvs.core :as hgvs])
(h2v/hgvs->vcf-variants #clj-hgvs/hgvs "NM_005228:c.2573T>G" "path/to/hg38.fa" "path/to/refGene.txt.gz")
;;=> ({:chr "chr7", :pos 55191822, :ref "T", :alt "G"})
(h2v/hgvs->vcf-variants #clj-hgvs/hgvs "c.2573T>G" "EGFR" "path/to/hg38.fa" "path/to/refGene.txt.gz")
;;=> ({:chr "chr7", :pos 55191822, :ref "T", :alt "G"})
(h2v/hgvs->vcf-variants #clj-hgvs/hgvs "p.A222V" "MTHFR" "path/to/hg38.fa" "path/to/refGene.txt.gz")
;;=> ({:chr "chr1", :pos 11796320, :ref "GG", :alt "CA"}
;; {:chr "chr1", :pos 11796320, :ref "GG", :alt "AA"}
;; {:chr "chr1", :pos 11796320, :ref "GG", :alt "TA"}
;; {:chr "chr1", :pos 11796321, :ref "G", :alt "A"})
```
### Finding HGVS aliases
`varity.hgvs/find-aliases` finds alternative HGVS expressions for the same
variant.
```clojure
(require '[varity.hgvs :as vhgvs])
(vhgvs/find-aliases #clj-hgvs/hgvs "NM_000059:c.162CAA[1]"
"path/to/hg38.fa" "path/to/refGene.txt.gz")
;;=> (#clj-hgvs/hgvs "NM_000059:c.162CAA[1]"
;; #clj-hgvs/hgvs "NM_000059:c.165_167delCAA")
```
### Conversion of a genomic coordinate between assemblies
To convert a genomic coordinate between assemblies,
```clojure
(require '[varity.lift :as lift])
(lift/convert-coord {:chr "chr1", :pos 743267} "path/to/hg19ToHg38.over.chain.gz")
;;=> {:chr "chr1", :pos 807887}
```
## License
Copyright 2017-2022 [Xcoo, Inc.](https://xcoo.jp/)
Licensed under the [Apache License, Version 2.0](LICENSE).
## Acknowledgements
The algorithm of `varity.fusion` was initially developed by Norio Tanaka at Cancer Precision Medicine Center, Japanese Foundation for Cancer Research. We thank him for his scientific insight and technical help.